Is B4GALNT3 p.Pro443Arg (c.1328C>G) pathogenic?

B4GALNT3 p.Pro443Arg (c.1328C>G) is classified Uncertain significance in B4GALNT3 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-05-08). AlphaMissense: likely benign (0.0948); Absent from gnomAD v4.1.

How common is B4GALNT3 p.Pro443Arg (c.1328C>G) in the general population?

B4GALNT3 p.Pro443Arg (c.1328C>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about B4GALNT3 p.Pro443Arg (c.1328C>G)?

AlphaMissense predicts likely benign (score 0.0948) — an in-silico prediction, not a clinical call.

B4GALNT3 p.Pro443Arg

c.1328C>G · VCV3259205

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0948 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0948	likely benign
REVEL	0.063	moderately benign-leaning
SaProt	LLR -6.71	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 1.1	GERP 0.66, phastCons 0.01
Regional constraint	o/e 0.89	unconstrained · MANE · 17 kb · p 0.00032 · regional, not allelic
Overall
CADD	17.5	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: B4GALNT3
Protein: p.Pro443Arg
Coding: c.1328C>G
MANE Select: NM_173593
Type: single nucleotide variant
Location: chr12:553251 (GRCh38)
Gene constraint: LOEUF 0.835 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 71.56

Full B4GALNT3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

B4GALNT3 p.Arg686= Benign ★★ same type
B4GALNT3 p.Glu441Asp Benign ★★ same type
B4GALNT3 p.Gly752Val Benign ★★ same type
B4GALNT3 p.His536Tyr Benign ★★ same type
B4GALNT3 c.1271-1G>C Likely pathogenic ★ same type
B4GALNT3 p.Ala158Ser Uncertain significance ★ ⚠ same type
B4GALNT3 p.Ala239Val Uncertain significance ★ ⚠ same type
B4GALNT3 p.Ala28Val Uncertain significance ★ ⚠ same type

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/b4galnt3-p-pro443arg (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown